What settings will preserve quality when I output an edited .mp4 for Youtube upload?
Work from the best quality sources you can, and keep the work in EXR stills format until you are ready to conform the work to a master.
BINAC: Blender Is Not An Encoder. The bulk of your issue here is largely because you are relying on the various encoding settings from within Blender. Blender is not and should not be considered an encoder. Work from step 1 and provide a series of still images that your conformer can work with. For example, outputting to 100% quality JPEGs from your EXRs and then encode them with FFMPEG. FFMPEG offers many preset configurations that will deliver results that are leaps and bounds better than Blender's encoding defaults, as well as provide you with the flexibility to encode shot by shot if required to a suitable format.


For more information as to the low level internals and the whys regarding the above, you can see an answer I have posted here. Good luck.